CBIcall
Reproducible germline variant calling for Illumina DNA sequencing
CBIcall (CNAG Biomedical Informatics framework for variant calling) gives users a single command-line entry point for curated WES, WGS, and mtDNA workflows, while keeping run configuration, logs, and outputs traceable.
In one sentence
CBIcall validates a parameters YAML file, resolves the requested workflow, creates a run directory, and launches the matching Bash or Snakemake pipeline.
What CBIcall Does
CBIcall is an orchestrator. It does not re-implement alignment or variant calling algorithms; it runs curated workflows built from established tools such as BWA, GATK, and MToolBox.
- validates the parameters YAML before launch
- dispatches Bash or Snakemake workflows
- records logs, provenance, run reports, and output fingerprints when available
Installation at a Glance
| Use case | Method |
|---|---|
| Local workstation or server | Docker |
| HPC cluster | Apptainer / Singularity |
| Development or debugging | From Source |
| Cloud reproducibility check | Google Cloud |
Where to Go Next
| Goal | Page |
|---|---|
| Run the shipped test data | Quickstart |
| Run WES/WGS data | WES Example |
| Run mtDNA analysis | mtDNA Example |
| Understand output files | Outputs |
| See the system design | Architecture |